Contacts of the strand formed by residues 1209 - 1214 (chain B) in PDB entry 1W21
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER1209 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A HIS* 5.8 0.9 - - - +
105A ILE* 5.9 1.0 - - - +
461A LEU* 4.0 36.6 - - - +
462A GLY 4.5 8.9 + - - -
1200B CYS 3.7 0.9 - - - +
1201B MET* 3.2 4.0 - - - -
1202B SER* 2.9 37.8 + - - -
1208B ALA* 1.3 76.8 - - - +
1210B ALA* 1.3 62.4 + - - +
1211B VAL* 5.1 6.1 - - - +
1222B ILE 3.3 11.9 - - - -
1223B PRO* 4.3 1.6 - - - -
1230B LEU* 4.1 4.7 - - - +
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Residues in contact with ALA1210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199B ILE* 4.0 12.6 - - + -
1200B CYS 3.4 5.4 - - - -
1201B MET* 3.9 29.4 - - + -
1209B SER* 1.3 74.9 - - - +
1211B VAL* 1.3 63.1 + - - +
1212B VAL* 4.2 0.9 - - + -
1221B GLU* 3.2 6.1 - - - +
1222B ILE* 2.8 52.2 + - + +
1230B LEU* 3.8 3.9 - - + +
1248B MET* 5.0 0.9 - - + -
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Residues in contact with VAL1211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A HIS* 3.7 47.8 - - + +
105A ILE* 4.1 19.5 - - + +
461A LEU* 5.6 0.2 - - + -
1182B CYS* 5.8 0.9 - - + -
1183B ILE 6.0 0.9 - - - +
1199B ILE* 3.5 2.2 - - - -
1200B CYS* 3.1 30.2 + - + +
1209B SER* 5.1 7.9 - - - +
1210B ALA* 1.3 77.3 - - - +
1212B VAL* 1.3 62.9 + - - +
1213B TRP* 3.3 34.3 - - + +
1218B PRO* 4.2 7.0 - - + -
1220B THR 3.3 8.7 - - - +
1221B GLU* 4.6 4.0 - - + -
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Residues in contact with VAL1212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197B MET* 3.9 28.3 - - + -
1198B SER 3.8 2.5 - - - -
1199B ILE* 3.9 17.0 - - + -
1210B ALA* 5.1 0.4 - - + -
1211B VAL* 1.3 76.5 - - - +
1213B TRP* 1.3 54.3 + - - +
1218B PRO* 3.7 1.2 - - - +
1219B ILE* 2.7 32.7 + - - +
1220B THR* 2.6 28.8 + - - +
1222B ILE* 4.2 12.6 - - + -
1264B PHE* 3.7 27.6 - - + -
1267B GLY* 3.8 22.0 - - - +
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Residues in contact with TRP1213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ILE 4.5 4.9 + - - -
106A LEU* 3.3 51.8 - - + -
169A MET* 4.0 18.4 - - + -
1180B VAL 6.1 0.2 - - - -
1181B GLU 3.7 15.9 - - - +
1182B CYS* 3.3 31.6 - - + +
1183B ILE 5.1 0.9 - - - +
1196B ARG 4.4 0.7 - - - -
1197B MET* 3.1 13.6 - - - +
1198B SER* 2.8 39.2 + - - +
1211B VAL* 3.3 35.5 - - + +
1212B VAL* 1.3 76.4 - - - +
1214B TYR* 1.4 61.3 + - - +
1216B GLY* 3.5 33.0 - - - +
1217B ARG 3.3 5.4 - - - +
1218B PRO* 3.6 23.6 - - + -
1219B ILE* 4.3 0.2 - - - -
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Residues in contact with TYR1214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090B PHE* 4.3 1.6 - - - -
1192B ASP* 2.5 36.0 + - - -
1194B MET* 3.9 7.6 - - - +
1195B SER* 3.4 33.9 + - - -
1196B ARG 3.5 10.5 - - - -
1197B MET* 4.1 12.1 - - + -
1213B TRP* 1.4 76.2 - - - +
1215B GLY* 1.3 66.6 + - - +
1216B GLY 3.0 1.3 - - - -
1217B ARG* 2.8 27.3 + - - +
1219B ILE* 3.5 21.3 - - + +
1244B CYS* 6.3 1.1 - - - -
1266B GLU* 3.6 54.8 + - + +
1267B GLY 3.9 3.6 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il